HIV invasion of the central nervous system (CNS) occurs early after infection. Viral adaptation to replication in the CNS and its immunologic sequelae results in clinical neuropathological sequelae in up to 50% of untreated patients. Both host and viral determinants may mediate the neuropathology that results in the clinical syndromes of HIV associated dementia (HIV-D) and minor motor cognitive disorder (MMCD). In this study, we will examine the rate and possible determinants of evolution of HIV-1 in the CNS through 3 specific aims. SA 1: HIV-1 gp160 and nef sequence evolution will be assessed by comparing plasma and CSF virus in untreated patients identified in primary infection that are followed over 3 to 5 years employing rapid and sensitive screening of length polymorphism in V1-2 A/4-5 of env and clonal sequence analysis of env and nef. Concurrently, blood and CSF virus comparisons will be performed on longitudinal samples from a cohort of patients with chronic infection over a 3 to 5 year period to provide. Where differences are found, machine learning algorithms and multiple regression analysis will be performed to identify individual positions that contribute to sequence evolution with attention to glycosylation sites that alter neutralization by antibody, V3 positions that affect tropism or putative neurotoxicity, and CTL epitopes described in both env and nef. SA 2: In well characterized autopsy samples, CSF, plasma, parenchymal brain regions, spleen, lymph node and colon will be examined for proviral DNA sequences and RNA sequences, in order to characterize the composition of the HIV population in CNS and to determine the subset of viral variants that are productively replicating. SA 3: Prototypical env sequences identified in SA 1 and 2 will be cloned into expression vectors and co- receptor density dependence and usage and antibody neutralization susceptibility will be assessed. Sequence change in putative HLA restricted CTL epitopes in nef and env will be correlated with patient HLA type. Together, these studies will begin to identify and characterize immunologic determinants of HIV evolution in the CNS.